Menu
GeneBe

13-76885945-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_138444.4(KCTD12):c.204G>A(p.Gln68=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00282 in 1,591,236 control chromosomes in the GnomAD database, including 121 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 61 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 60 hom. )

Consequence

KCTD12
NM_138444.4 synonymous

Scores

1
1

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.01
Variant links:
Genes affected
KCTD12 (HGNC:14678): (potassium channel tetramerization domain containing 12) Enables identical protein binding activity. Predicted to be involved in protein homooligomerization. Predicted to act upstream of or within regulation of G protein-coupled receptor signaling pathway. Predicted to be located in cell projection. Predicted to be part of receptor complex. Predicted to be active in postsynaptic membrane and presynaptic membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 13-76885945-C-T is Benign according to our data. Variant chr13-76885945-C-T is described in ClinVar as [Benign]. Clinvar id is 786241.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.01 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0503 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCTD12NM_138444.4 linkuse as main transcriptc.204G>A p.Gln68= synonymous_variant 1/1 ENST00000377474.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCTD12ENST00000377474.4 linkuse as main transcriptc.204G>A p.Gln68= synonymous_variant 1/1 NM_138444.4 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0145
AC:
2212
AN:
152236
Hom.:
60
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0493
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00824
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000620
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.0110
GnomAD3 exomes
AF:
0.00347
AC:
742
AN:
214122
Hom.:
24
AF XY:
0.00267
AC XY:
318
AN XY:
119152
show subpopulations
Gnomad AFR exome
AF:
0.0499
Gnomad AMR exome
AF:
0.00218
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000105
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000113
Gnomad OTH exome
AF:
0.00167
GnomAD4 exome
AF:
0.00157
AC:
2259
AN:
1438882
Hom.:
60
Cov.:
31
AF XY:
0.00137
AC XY:
978
AN XY:
716074
show subpopulations
Gnomad4 AFR exome
AF:
0.0524
Gnomad4 AMR exome
AF:
0.00293
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000142
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000848
Gnomad4 OTH exome
AF:
0.00459
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0146
AC:
2223
AN:
152354
Hom.:
61
Cov.:
33
AF XY:
0.0145
AC XY:
1082
AN XY:
74508
show subpopulations
Gnomad4 AFR
AF:
0.0494
Gnomad4 AMR
AF:
0.00823
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.0109
Alfa
AF:
0.00179
Hom.:
3
Bravo
AF:
0.0166
Asia WGS
AF:
0.00346
AC:
12
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJun 18, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
Cadd
Benign
13
Dann
Uncertain
0.97

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs116710456; hg19: chr13-77460080; COSMIC: COSV58524911; COSMIC: COSV58524911; API